Schema for intronEst

Database: droVir2 Primary Table: intronEst Row Count: 15,604 Data last updated: 2016-03-29
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`bin`	585	`smallint(5) unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	440	`int(10) unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	0	`int(10) unsigned`	range	Number of bases that don't match
`repMatches`	0	`int(10) unsigned`	range	Number of bases that match but are part of repeats
`nCount`	0	`int(10) unsigned`	range	Number of 'N' bases
`qNumInsert`	1	`int(10) unsigned`	range	Number of inserts in query
`qBaseInsert`	1	`int(10) unsigned`	range	Number of bases inserted in query
`tNumInsert`	1	`int(10) unsigned`	range	Number of inserts in target
`tBaseInsert`	67	`int(10) unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	CX159220	`varchar(255)`	values	Query sequence name
`qSize`	441	`int(10) unsigned`	range	Query sequence size
`qStart`	0	`int(10) unsigned`	range	Alignment start position in query
`qEnd`	441	`int(10) unsigned`	range	Alignment end position in query
`tName`	scaffold_10322	`varchar(255)`	values	Target sequence name
`tSize`	456894	`int(10) unsigned`	range	Target sequence size
`tStart`	60961	`int(10) unsigned`	range	Alignment start position in target
`tEnd`	61468	`int(10) unsigned`	range	Alignment end position in target
`blockCount`	3	`int(10) unsigned`	range	Number of blocks in alignment
`blockSizes`	51,270,119,	`longblob`		Size of each block
`qStarts`	0,52,322,	`longblob`		Start of each block in query.
`tStarts`	60961,61012,61349,	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	droVir2.all_est.qName (via intronEst.qName) droVir2.estOrientInfo.name (via intronEst.qName) hgFixed.gbCdnaInfo.acc (via intronEst.qName) hgFixed.gbSeq.acc (via intronEst.qName) hgFixed.imageClone.acc (via intronEst.qName)

Sample Rows

bin	matches	misMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
585	440	0	0	1	1	1	67	-	CX159220	441	441	scaffold_10322	456894	60961	61468	3	51,270,119,	0,52,322,	60961,61012,61349,
587	697	0	0	0	0	2	1512	-	CX159602	697	697	scaffold_10322	456894	380992	383201	3	417,209,71,	0,417,626,	380992,382920,383130,
587	661	2	0	1	1	3	1513	-	CX159593	664	664	scaffold_10322	456894	381025	383201	5	72,4,307,209,71,	0,72,77,384,593,	381025,381098,381102,382920,383130,
585	595	9	1	0	0	2	240	-	CX159555	605	605	scaffold_12420	7302	1075	1920	3	142,354,109,	0,142,496,	1075,1276,1811,
589	518	1	0	0	0	2	214	+	CX159329	519	519	scaffold_12723	5800522	611014	611747	3	10,76,433,	0,10,86,	611014,611175,611314,
589	619	2	0	1	1	2	214	+	CX159610	626	622	scaffold_12723	5800522	611014	611849	4	10,76,523,12,	0,10,86,610,	611014,611175,611314,611837,
602	653	3	0	0	0	1	237	+	CX159373	656	656	scaffold_12723	5800522	2320463	2321356	2	35,621,	0,35,	2320463,2320735,
604	715	1	0	1	1	4	4130	-	CX159613	717	717	scaffold_12723	5800522	2493216	2498062	6	70,27,4,542,66,7,	0,70,97,102,644,710,	2493216,2496712,2496740,2496744,2497693,2498055,
604	692	0	0	0	0	3	4129	-	CX159488	692	692	scaffold_12723	5800522	2493241	2498062	4	45,574,66,7,	0,45,619,685,	2493241,2496712,2497693,2498055,
604	614	0	0	0	0	2	703	-	CX159371	614	614	scaffold_12723	5800522	2496745	2498062	3	541,66,7,	0,541,607,	2496745,2497693,2498055,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.